Methods to Monitor Post-Translational Gene Silencing Activity in Plant Tissues/Cell Types Relevant for Pathogen Entry, Propagation or Replication

ABSTRACT

The invention relates to transgenic plants comprising an inverted-repeat construct which triggers post-transcriptional gene silencing of an endogenous visual reporter gene driven by a tissue-specific promoter wherein said tissue is relevant for pathogen entry, propagation or replication and their uses for screening natural or synthetic molecules, microorganisms or extracts from micro- or macro-organisms for their potential ability to inhibit pathogen entry, propagation or replication in plants by enhancing PTGS or for characterizing the mode of action of natural or synthetic molecules that are known to enhance plant disease resistance through an ill-defined mode of action.

The present invention pertains to the field of agriculture. The invention relates to a method to monitor post-transcriptional gene silencing (PTGS) activity triggered by inverted-repeat in plant tissues/cell types that are relevant for the entry, propagation or replication of phytopathogens. These reporter systems can for instance be used to characterize the modes of action of known natural/synthetic compounds, microorganisms or extracts from micro- or macro-organisms that are known to promote disease resistance in crops. In addition, these reporter lines can be used to identify novel natural/synthetic compounds, microorganisms or extracts from micro- or macro-organisms that can promote PTGS and likely increase disease resistance in various cultivated plants.

BACKGROUND AND STATE OF THE ART

The innate immune response is the first line of defense against pathogens, and plays a critical role in antimicrobial defence. This response is initiated by host-encoded Pattern-Recognition Receptors (PRRs) that recognize evolutionarily conserved pathogen-derived signatures, known as Microbe-Associated Molecular Patterns (MAMPs), and activate MAMP-triggered immunity (MTI) (Boller & Felix, 2009). Furthermore, plants have evolved another strategy to perceive microbial pathogens through disease resistance (R) proteins, which recognize, directly or indirectly, divergent pathogen virulence determinants known as effector proteins, and establish effector-triggered immunity (ETI) (Jones & Dangl, 2006). Upon detection of MAMPs or pathogen effectors, plant cells rapidly induce a series of signalling events that involve for instance, the differential expression of short interfering RNAs (siRNAs) and microRNAs (miRNAs) (Pumplin N & Voinnet O, 2013). Recently, several siRNAs and miRNAs were found to orchestrate MTI and ETI responses (Weiberg et al., 2014), implying a key role of RNA silencing in the regulation of the plant immune system.

RNA silencing is an ancestral gene regulatory mechanism that controls gene expression at the transcriptional (TGS, Transcriptional Gene Silencing) and post-transcriptional (PTGS, Post-transcriptional Gene Silencing) levels. In plants, this mechanism has been initially characterized in antiviral resistance (Hamilton & Baulcombe, 1999). The core mechanism of RNA silencing starts with the production of double stranded RNAs (dsRNAs) that are processed by RNase-III enzymes DICERs into 20-24 nt small RNA duplexes that subsequently associate with an Argonaute (AGO) protein, which represent the central component of the RNA-induced silencing complexes (RISC). One strand, the guide, remains bound to the AGO effector protein to regulate genes in a mature RISC, while the other strand, the passenger, is degraded. The plant model Arabidopsis thaliana encodes 4 DICER-like proteins and 10 AGOs. DCL1 processes miRNA precursors into miRNA/miRNA* duplexes and the guide miRNA strand directs AGO1-RISC to sequence complementary mRNA targets to trigger their degradation and/or translation inhibition. DCL2 and DCL4 are involved in the biogenesis of short interfering RNAs (siRNAs) derived from viral dsRNAs and play a critical role in antiviral resistance (Deleris et al., 2006; Diaz-Pendon et al., 2007). These DICER-like proteins are also involved, together with DCL3, in the production of siRNAs derived from transposable elements, read through, convergent or overlapping transcription, endogenous hairpins as well as some miRNA precursors (Bologna & Voinnet, 2014). In addition, a large proportion of dsRNAs are produced by RNA-dependent RNA polymerases (RDRs) that convert single stranded RNAs into dsRNAs. RDR6, which is one out of six Arabidopsis RDRs, produces dsRNAs from viral, transgene transcripts as well as some endogenous transcripts including transposable elements (Mourrain et al., 2000; Dalmay et al, 2000.; Schwach et al., 2005; Xie et al., 2004). These dsRNAs are processed in part by DCL4 and DCL2 into 21 nt and 22 nt siRNAs, respectively, which direct PTGS of endogenous sequence complementary mRNA targets or exogenous RNAs derived from sense-transgenes or viral RNAs (Bologna & Voinnet, 2014). Furthermore, both siRNA and miRNA duplexes are methylated by the small RNA methyltransferase HEN1 and this modification is essential for their stability (Yu et al, 2005; Li et al., 2005; Chen et al., 2012).

Although endogenous miRNAs and siRNAs were initially characterized in various plant development processes, they have more recently emerged as key regulators of the plant innate immune response (Pumplin & Voinnet, 2013). For instance, the miR393 is a conserved microRNA that is induced during MTI and that contributes to antibacterial resistance in Arabidopsis (Navarro et al., 2006, 2008; Fahlgren et al., 2007; Li et al., 2010). Furthermore, phenotypical analyses in mutants that are defective in PTGS exhibit enhanced disease susceptibility to fungal, bacterial and oomycete pathogens (Navarro et al., 2008; Qiao et al., 2013; Ellendorff U et al., 2009; Navarro & Voinnet, 2008 WO/2008/087562), supporting a central role of this gene regulatory process in resistance against unrelated pathogens. However, despite the well-established role of RNA silencing in resistance against viral and non-viral pathogens, very little is known on the physiological relevance, or on the activity, of RNA silencing in tissues that are relevant for the entry and/or propagation of phytopathogens.

Phytopathogenic microbes can be divided into biotrophs, hemibiotrophs and necrotrophs according to their different lifestyles. Biotrophic pathogens can take-up nutrients from living host cells and maintain host cell viability, while necrotrophs kill host cells and feed on dead tissues. Hemibiotrophs use an early biotrophic phase followed by a necrotrophic phase. These phytopathogenic microbes use different strategies to enter inside host tissues. The majority of fungal and oomycete pathogens first produce spores, which adhere to the plant surface and further germinate to form a germ tube. Subsequently, the germ tube develops an appressorium that can perforate, through a penetration peg, the cuticle and cell wall layer through mechanical forces (Horbach et al., 2011) and therefore enter inside host tissues. Once inside plant tissues, the hyphal tip forms a second specialized structure referred to as the haustorium that can uptake nutrients from host cells but also represents a major site of pathogen effector secretion (Mendgen & Hahn, 2002; Horbach et al., 2011). Other pathogens do not perforate the cuticle cell wall layer but instead use natural openings to reach internal host tissues. For instance, hemibiotrophic bacterial pathogens such as Pseudomonas and Xanthomonas use hydathodes, stomata or woundings as natural entry sites for their endophytic colonization (Dou & Zhou, 2012). These bacterial pathogens can also enter plant tissues through the base of trichomes in some instances (Xin & He, 2013). Some fungal pathogens can also use natural openings to enter plant tissues. For example, Cladosporium fulvum colonizes internal host tissues through stomatal openings by forming long, branched intercellular hyphal structures with no obvious haustorium (Thomma et al., 2005). It is therefore not surprising that plants have evolved sensitive pathogen recognition mechanisms, and sophisticated defense responses, in these tissues/cell types to prevent pathogen entry (Melotto et al., 2006; Hugouvieux et al., 1998). As an example, plants can perceive bacterial MAMPs at the level of guard cells and in turn trigger stomatal closure, which efficiently controls the access of bacterial pathogens to internal host tissues (Melotto et al., 2006). Active defense responses have also been reported at hydathodes and at the base of trichomes (Hugouvieux et al., 1998; Yu et al., 2013; Frerigmann et al., 2012; Jakoby et al., 2008), although very little is known on the detailed mechanisms that orchestrate such local innate immune responses.

Once inside the intercellular space of plant leaves, biotrophic and hemibiotrophic pathogens use different strategies to colonize distal plant tissues. For example, RNA viruses use alive phloem tissues as a major route to propagate in systemic tissues and this viral spreading is restricted by PTGS. As an example, Arabidopsis mutants that are defective in the two major antiviral Dicer-like 2 (DCL2) and DCL4 exhibit long distance propagation of several RNA viruses (Deleris et al., 2006; Diaz-Pendon et al., 2007). By contrast, fungal, oomycete and bacterial pathogens can spread in distal plant tissues through xylem vessels, which are dead cells that transport nutrients and water from the root to the aerial part of the plant. The plant defense responses that restrict vascular spreading involve multiple processes including, for instance, the production of reactive oxygen species (ROS) and antimicrobial proteins from adjacent xylem parenchyma cells, the plant-induced physical obstruction of vascular vessels through lignification, the efficient recognition of pathogen effectors through R proteins (Guy et al., 2013). However, it is not known whether PTGS plays any role in restricting the propagation of such non-viral pathogens within and around xylem vessels.

In the present invention, the inventors first provide experimental evidence that PTGS plays a critical role in controlling the entry of a virulent Pseudomonas syringae strain at the level of hydathodes and stomata in Arabidopsis thaliana. Furthermore, they show that PTGS efficiently restricts vascular propagation of this pathogenic bacterium in Arabidopsis leaf vasculature. Based on these observations, they have selected the most relevant promoters that are active enough in dedicated tissues or cell types to generate a whole series of visual inverted repeat PTGS reporter lines in the model plant Arabidopsis thaliana. These PTGS reporter lines are based on the tissue-specific silencing of an endogenous gene involved in chlorophyll biosynthesis and therefore allow an easy monitoring of PTGS activity in tissues/cell types that are relevant for pathogen entry, propagation or replication, namely the hydathodes, guard cells, epidermal cells, xylem parenchyma cells, cells at the base of trichomes, phloem companion cells and mesophyll cells.

The intended applications therefore deal with methods to increase disease resistance in cultivated plants by enhancing PTGS activity in tissues/cell types that are relevant for pathogen entry, propagation or replication. For instance, they can be used for high-throughput screening of natural or synthetic compounds that can enhance the chlorotic phenotype and likewise promote PTGS in tissues/cell types that are physiologically relevant for plant disease management. Given the critical and widespread role of PTGS in plant disease resistance, the identified PTGS inducer compounds will likely enhance resistance against unrelated pathogens in Arabidopsis but also in agriculturally important crops by preventing pathogen entry, propagation and/or replication. As a proof-of-concept experiment, the inventors have challenged these PTGS sensors with commercially available natural or synthetic—active or formulated—compounds that are known to increase disease resistance in cultivated plants. Results from these analyses indicated that well-characterized compounds can indeed promote PTGS on one specific silencing reporter. Besides providing novel insights into the mode of action of these commercially available molecules, these experiments indicate that such PTGS reporters can be exploited to conduct high-throughput screening in order to identify novel natural/synthetic compounds, microorganisms or extracts from micro- or macro-organisms that have the potential to promote disease resistance in cultivated plants by enhancing PTGS activity. Furthermore, such reporter system can also be used to elucidate the mode of action of compounds, microorganisms or extracts from micro- or macro-organisms with known antimicrobial activity in order to meet the requirement of the legislation for their commercialization.

SUMMARY

The subject-matter of the present invention is thus a method for screening natural or synthetic molecules, microorganisms or extracts from micro- or macro-organisms for their potential ability to inhibit pathogen entry, propagation or replication in plants through PTGS enhancement comprising the following steps:

-   -   (a) providing visual PTGS reporter plants transgenic for an         inverted-repeat construct which triggers post-transcriptional         gene silencing of an endogenous visual reporter gene driven by a         tissue-specific promoter wherein said tissue is relevant for         pathogen entry, propagation or replication,     -   (b) applying said molecules or microorganisms or extracts on         said plants,     -   (c) visually observing plant changes translating an increase or         decrease of said post-transcriptional gene silencing activity of         said endogenous visual reporter gene.

Another subject-matter of the present invention is a method for characterizing the mode of action of natural or synthetic molecules, microorganisms or extracts from micro- or macro-organisms that are known to enhance plant disease resistance comprising the following steps:

-   -   (a) providing several types of visual PTGS reporter plants         transgenic for an inverted-repeat construct which triggers         post-transcriptional gene silencing of an endogenous visual         reporter gene, each type driven by a different tissue-specific         promoter wherein said tissue is relevant for pathogen entry,         propagation or replication,     -   (b) applying said molecules or microorganisms or extracts on         said plants,     -   (c) visually observing plant changes translating an increase or         decrease of said post-transcriptional gene silencing activity of         said endogenous visual reporter gene in one or several of said         types of visual PTGS reporter plants.

Another subject-matter of the present invention is a transgenic plant comprising an inverted-repeat construct which triggers post-transcriptional gene silencing of an endogenous visual reporter gene driven by a tissue-specific promoter wherein said tissue is relevant for pathogen entry, propagation or replication.

Another subject-matter of the present invention is an isolated DNA with a hairpin structure comprising an inverted-repeat construct which triggers post-transcriptional gene silencing of an endogenous visual reporter gene under the control of a tissue-specific promoter.

Another subject-matter of the present invention is a vector comprising isolated DNA with a hairpin structure under the control of a promoter according to the invention.

Definitions

To “modulate” means to inhibit or to increase.

A “visual reporter gene” means a gene linked to a visual phenotype upon silencing of the said endogenous gene. Modulation of its expression is directly visualized by a phenotypic change that is detected with naked eyes.

A “tissue-specific promoter” means here a promoter that allows the expression of the inverted repeat exclusively in said tissue and with an activity that is strong enough to allow the visual detection of phenotypic changes upon silencing of an endogenous visual reporter gene.

A “tissue relevant for pathogen entry” means a tissue through which the pathogen enters in the host organism.

A “tissue relevant for pathogen propagation” means a tissue composing, or in the proximity of, the routes required for short or long distance pathogen colonization in plants.

An “extract” means the result of a chemical or physical process on a mixture or material, for example all or part of a macroorganism, preferably a plant, or a microorganism population, preferably an in vitro microorganism culture. The term “extract” comprises isolated natural molecules and compounds.

RNA silencing or interference (RNAi) is a valuable reverse genetics tool to study gene function in various organisms. The process of RNAi was initially described as a post-transcriptional gene silencing mechanism of gene regulation.

With the RNAi method, double-stranded RNA (dsRNA) can specifically lower the products—mRNA and/or protein—of a target gene when introduced into, or expressed from, an organism or cells derived from such organism. RNAi involves the processing of dsRNA precursors into short interfering RNA (siRNA) duplexes of approximately 21 to 24 nucleotides in length by Dicer enzymes, named DICER-like enzymes in plants. A selected strand, referred to as the guide strand, is incorporated into a RNA-induced silencing complex (RISC) containing an AGO protein, which is the catalytic component of RISC. The small RNA guide strand directs RISC onto sequence complementary mRNA targets to trigger their degradation and/or translational inhibition.

“Homology” is defined as the percentage of bases in the nucleotide sequence variant that are identical after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent homology. Methods and computer programs for the alignment are well known in the art. One such computer program is “Align 2”, authored by Genentech, Inc., which was filed with user documentation in the United States Copyright Office, Washington, D.C. 20559, on Dec. 10, 1991.

An “isolated” molecule is one that has been identified and separated and/or recovered from a component of its natural environment.

The terms “polypeptide”, “peptide” or “protein” are used interchangeable throughout this specification.

To determine the percentage of homology between two amino acid sequences (e.g., one of the sequences encoded by a nucleic acid of the invention and a mutant form thereof) or of two nucleic acids, the sequences are aligned for optimal comparison purposes (e.g., gaps can be introduced in the sequence of one protein or nucleic acid for optimal alignment with the other protein or nucleic acid). The amino acid residues or nucleotides at corresponding amino acid positions or nucleotide positions are then compared. When a position in one sequence is occupied by the same amino acid residue or nucleotide as the corresponding position in the other sequence, then the molecules are homologous at that position (i.e., as used herein amino acid or nucleic acid “homology” is equivalent to amino acid or nucleic acid “identity”). The percent homology between the two sequences is a function of the number of identical positions shared by the sequences (i.e., % homology=numbers of identical positions/total numbers of positions×100).

An “isolated” nucleic acid molecule is one molecule, which is substantially separated from other nucleic acid molecules, which are present in the natural source of the nucleic acid. Preferably, an “isolated” nucleic acid is substantially free of sequences that naturally flank the nucleic acid (i.e., sequences located at the 5′ and 3′ ends of the nucleic acid) in the genomic DNA of the organism, from which the nucleic acid is derived.

Moreover, the term “polynucleotide” as used in accordance with the present invention encompasses variants of the aforementioned specific polynucleotides. Said variants may represent orthologs, paralogs or other homologs of the polynucleotide of the present invention. The polynucleotide variants, preferably, also comprise a nucleic acid sequence characterized in that the sequence can be derived by at least one nucleotide substitution, addition and/or deletion whereby the variant nucleic acid sequence shall still encode a polypeptide having a biological activity as specified above. Variants also encompass polynucleotides comprising a nucleic acid sequence which is capable of hybridizing to the aforementioned specific nucleic acid sequences, preferably, under stringent hybridization conditions. These stringent conditions are known to the skilled worker and can be found in Current Protocols in Molecular Biology, John Wiley & Sons, N. Y. (1989), 6.3.1-6.3.6. A preferred example for stringent hybridization conditions are hybridization conditions in 6× sodium chloride/sodium citrate (=SSC) at approximately 45° C., followed by one or more wash steps in 0.2×SSC, 0.1% SDS at 50 to 65° C. The skilled worker knows that these hybridization conditions differ depending on the type of nucleic acid and, for example when organic solvents are present, with regard to the temperature and concentration of the buffer. For example, under “standard hybridization conditions” the temperature differs depending on the type of nucleic acid between 42° C. and 58° C. in aqueous buffer with a concentration of 0.1 to 5×SSC (pH 7.2). If organic solvent is present in the abovementioned buffer, for example 50% formamide, the temperature under standard conditions is approximately 42° C. The hybridization conditions for DNA:DNA hybrids are, preferably, 0.1×SSC and 20° C. to 45° C., preferably between 30° C. and 45° C. The hybridization conditions for DNA:RNA hybrids are, preferably, 0.1×SSC and 30° C. to 55° C., preferably between 45° C. and 55° C. The abovementioned hybridization temperatures are determined for example for a nucleic acid with approximately 100 bp (=base pairs) in length and a G+C content of 50% in the absence of formamide. The skilled worker knows how to determine the hybridization conditions required by referring to textbooks such as the textbook mentioned above, or the following textbooks: Sambrook et al., “Molecular Cloning”, Cold Spring Harbor Laboratory, 1989; Hames and Higgins (Ed.) 1985, “Nucleic Acids Hybridization: A Practical Approach”, IRL Press at Oxford University Press, Oxford; Brown (Ed.) 1991, “Essential Molecular Biology: A Practical Approach”, IRL Press at Oxford University Press, Oxford. Alternatively, polynucleotide variants are obtainable by PCR-based techniques such as mixed oligonucleotide primer-based amplification of DNA, i.e. using degenerated primers against conserved domains of the polypeptides of the present invention.

A fragment as meant herein, preferably, comprises at least 20, at least 50, at least 100, at least 250 or at least 500 consecutive nucleotides of any one of the aforementioned nucleic acid sequences or encodes an amino acid sequence comprising at least 20, at least 30, at least 50, at least 80, at least 100 or at least 150 consecutive amino acids of any one of the aforementioned amino acid sequences. Variant polynucleotides as referred to in accordance with the present invention may be obtained by various natural as well as artificial sources. For example, polynucleotides may be obtained by in vitro and in vivo mutagenesis approaches using the above mentioned specific polynucleotides as a basis. Moreover, polynucleotide being homologs or orthologs may be obtained from various species.

Binding as meant in this context refers to hybridization by Watson-Crick base pairing discussed elsewhere in the specification in detail. An oligonucleotide as used herein has a length of at most 100, at most 50, at most 40, at most 30 or at most 20 nucleotides in length which are complementary to the nucleic acid sequence of the polynucleotides of the present invention. The sequence of the oligonucleotide is, preferably, selected so that a perfect match by Watson-Crick base pairing will be obtained. The oligonucleotides of the present invention may be suitable as primers for PCR-based amplification techniques.

The term “dsRNA” refers to RNA having a duplex structure comprising two complementary and anti-parallel nucleic acid strands. Not all nucleotides of a dsRNA necessarily exhibit complete Watson-Crick base pairs; the two RNA strands may be substantially complementary. The RNA strands forming the dsRNA may have the same or a different number of nucleotides, with the maximum number of base pairs being the number of nucleotides in the shortest strand of the dsRNA. Preferably, the dsRNA is no more than 500, more preferably less than 400, and most preferably between 200 and 350, nucleotides in length. dsRNAs of this length are particularly efficient in inhibiting the expression of the target gene using inverted-repeat PTGS techniques. dsRNAs are subsequently processed by DCL enzymes into short interfering RNAs (siRNAs). RNAi is mediated by short interfering RNAs (siRNAs). The term “short interfering RNA” or “siRNA” refers to a nucleic acid molecule which is a double-stranded RNA agent that is complementary to i.e., able to base-pair with, a portion of a target RNA (generally mRNA), i.e. the polynucleotide of the present invention being RNA. siRNA molecules specifically guide RISC to silence the sequence complementary mRNA target. By virtue of the specificity of the siRNA sequence and its homology to the RNA target, siRNA is able to cause cleavage and/or translational inhibition of the target RNA strand, thereby promoting its degradation and inhibiting mRNA translation. Preferably, the siRNA duplex which is sufficient to mediate RNAi comprises a duplex of nucleic acid sequence fragments of the coding region of the targeted candidate gene. Also preferably, a nucleic acid sequence encoding a siRNA or dsRNA (e.g. 250 bp) comprising a sequence sufficiently complementary to a target gene is operatively linked to an expression control sequence. Thus, the mediation of RNAi to inhibit expression of the target gene can be modulated by said expression control sequence.

The complementary regions of the siRNA or dsRNA allow sufficient hybridization of the siRNA or dsRNA to the target mRNA and thus mediate RNAi. The siRNA sequence needs to be of sufficient length to bring the siRNA and target RNA together through complementary base-pairing interactions. The siRNA used may be of varying lengths. The length of the siRNA is preferably greater than or equal to ten nucleotides and of sufficient length to stably interact with the target RNA; specifically 15-30 nucleotides; more specifically any integer between 15 and 30 nucleotides, most preferably 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, and 30. By “sufficient length” is meant an oligonucleotide of greater than or equal to 15 nucleotides that is of a length long enough to provide the intended function under the expected condition. By “stably interact” is meant interaction of the short interfering RNA with target nucleic acid (e.g., by forming hydrogen bonds with complementary nucleotides in the target under physiological conditions). Generally, such complementarity is 100% between the siRNA and the RNA target, but can be less if desired, preferably 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%. For example, 19 bases out of 21 bases may be base-paired. In some instances, where selection between various allelic variants is desired, 100% complementary to the target gene is required in order to effectively discern the target sequence from the other allelic sequence. When selecting between allelic targets, choice of length is also an important factor because it is the other factor involved in the percent complementary and the ability to differentiate between allelic differences.

Down-regulation as meant herein relates to a statistically significant reduction of the mRNA detectable in a cell, tissue or organism or even to a failure to produce mRNA in detectable amounts at all. This also includes the reduction of the stability of mRNA encoding all or a part of any sequence described herein. Moreover, down-regulation also encompasses an impaired, i.e. significantly reduced, production of protein from RNA sequences encoding all or a part of any sequence or even the absence of detectable protein production.

A “transgenic plant” is defined herein as a plant which is genetically modified in some way. The altered genetic material may encode a protein comprising a regulatory or control sequence or may be or include an antisense sequence or encode an antisense RNA or siRNA which inhibits the DNA or mRNA sequence or portion thereof responsible of the expression of the polypeptide of which a modification of the expression is foreseen.

A “transgene” or “transgenic sequence” is defined as a foreign gene or partial sequence which has been incorporated into a transgenic plant.

Transgenic plants made in accordance with the present invention may be prepared by DNA transformation using any method of plant transformation known in the art. Plant transformation methods include direct co-cultivation of plants, tissues or cells with Agrobacterium tumefaciens or direct infection; direct gene transfer into protoplasts or protoplast uptake; electroporation; particle bombardment; injection into meristematic tissues of seedlings and plants; injection into protoplasts of cultured cells and tissues. Generally a complete plant is obtained from the transformation process. Plants are regenerated from protoplasts, callus, tissue parts or explants, etc.

The term “microorganisms” comprises plant pathogen microorganisms and non-plant pathogen microorganisms.

The term “pathogen” means any disease producing agent, for example bacteria, fungi, oomycetes, viruses and compounds released or secreted from these pathogens or from parasites, for example effectors injected by insects or nematodes.

LEGENDS OF FIGURES

FIG. 1. H₂O₂ production upon bacteria perception is localized in tissues relevant for entry (hydathodes and stomata) and for bacterial propagation (vascular tissues).

H₂O₂ production as detected by DAB (diaminobenzedine) staining in WT plant after water (Mock) or Pseudomonas fluorescens infiltration at the level of stomata (A), hydathodes (B) and veins (C), respectively

FIG. 2. PTGS-defective mutants exhibit a more pronounced entry and propagation of a virulent Pseudomonas syringae strain.

A. Wild type (WT) plants, hen1 and grp7-1 were sprayed with Pto-DC3000-GFP at 2·10⁷ cfu/ml. GFP was monitored under UV light 2 day after inoculation.

B. Five-week-old plants of WT, rdr6-15 and dcl2dcl4 mutants were wound-inoculated with a toothpick in secondary veins (white circle) with Pto-DC3000-GFP at 5·10⁷ cfu/ml. GFP is monitored under UV light at 5 day-post inoculation (dpi).

C. Five-week-old plants of WT, rdr6-1.5 and dcl2dcl4 mutants were wound-inoculated as in B. Pictures of bacterial disease symptoms were taken at 5 dpi.

FIG. 3. Phenotypes of some tissue/cell type-specific IR-PTGS sensors.

A. Schematic representation of the hairpin IR-SUL under the control of a tissue- or cell type-specific promoter

B. Phenotypes of representative T1 transgenic plants expressing the hairpin IR-SUL (SUL-LUS) under the control of a cambium-specific promoter (WOX4-p), xylem-specific promoters (AAP6-p and IRX3-p), hydathode-specific promoter (miR164A-p) and guard cell-specific promoter (GC1-p).

FIG. 4. Formulated Fosetyl-Al and laminarine compounds enhance PTGS activity at within and around phloem companion cells.

A. Pictures of 5-week-old SUC-SUL plants treated for 4 days with formulated fosetyl-Aluminium referred to as Aliette

B. Pictures of 5-week-old SUC-SUL plants treated for 4 days with formulated Laminarine.

C. Pictures of 5-week-old SUC-SUL plants treated for 4 days with formulated Bacillus subtilis.

FIG. 5. Molecular analysis on the SUC-SUL plants treated with salicylic acid.

A. Pictures of 5-week-old SUC-SUL plants treated either Mock (0.01% Silwet L-77 only) or 2 mM of SA (with 0.01% Silwet L-77) for 5 days.

B. RT-qPCR analysis depicting SUL and CIP4 transcript levels in SUC-SUL leaves treated with either Mock (0.01% Silwet L-77 only) or with 2 mM of SA (+0.01% Silwet L-77) for 3 days.

C. Western blot analyses showing SUL and CIP4 protein levels in SUC-SUL leaves treated with either Mock (0.01% Silwet L-77 only) or with 2 mM of SA (+0.01% Silwet L-77) for 3 days.

FIG. 6. Salicylic acid (SA) promotes PTGS activity within and around companion cells of the phloem but not in other tested tissue.

Picture of 5-week-old SUC-SUL, HYD-p::SUL-LUS, AAP6-p::SUL-LUS, IRX3-p::SUL-LUS or GC1-p::SUL-LUS plants treated either Mock (0.02% Silwet L-77 only) or 2 mM of SA (with 0.02% Silwet L-77) for 5 days.

DETAILED DESCRIPTION

The first subject-matter of the invention is a method for screening natural or synthetic molecules, microorganism and extracts from micro- or macro-organisms for their potential ability to inhibit pathogen entry, propagation or replication in plants through PTGS enhancement comprising the following steps:

-   -   (a) providing visual PTGS reporter plants transgenic for an         inverted-repeat construct which triggers post-transcriptional         gene silencing of an endogenous visual reporter gene driven by a         tissue-specific promoter wherein said tissue is relevant for         pathogen entry, propagation or replication,     -   (b) applying said molecules or microorganisms or extracts on         said plants,     -   (c) visually observing plant changes translating an increase or         decrease of said post-transcriptional gene silencing activity of         said endogenous visual reporter gene.

Non-limitative examples of microorganisms (or their extracts) which can be screened for a modulation of RNA silencing activity using the method of the invention include:

Acetobacteraceae, Acidobacteriaceae, Actinospicaceae, Actinosynnemataceae, Addliaceae, Alcaligenaceae, Alicyclobacillaceae, Alteromonadaceae, Ardenscatenaceae, Aurantimonadaceae, Bacillaceae, Bacteriovoracaceae, Bartonellaceae, Bdellovibrionaceae, Beijerinckiaceae, Bradyrhizobiaceae, Brevibacteriaceae, Brucellaceae, Burkholderiaceae, Burkholderiales, Burkholderiales_incertae_sedis, Caldicoprobacteraceae, Caulobacteraceae, Cellulomonadaceae, Chitinophagaceae, Chloracidobacteria, Chloroflexaceae, Clostridiaceae, Comamonadaceae, Conexibacteraceae, Coxiellaceae, Cryomorphaceae, Cystobacteraceae, Cystobacterineae, Cytophagaceae, Deinococcaceae, Dermacoccaceae, Enterobacteriaceae, Enterococcaceae, Erythrobacteraceae, Eubacteriaceae, Exiguobacteraceae, Fimbriimonadaceae, Flavobacteriaceae, Frankiaceae, Gaiellaceae, Geobacteraceae, Geodermatophilaceae, Glycomycetaceae, Gracilibacteraceae, Haliangiaceae, Haloplasmataceae, Holophagaceae, Hyphomicrobiaceae, Hyphomonadaceae, Intrasporangiaceae, Kineosporiaceae, Koribacteraceae, Kouleothrixaceae, Lachnospiraceae, Leptospiraceae, Methylobacteriaceae, Methylo cystaceae, Methylophilaceae, Microbacteriaceae, Micrococcaceae, Micromonosporaceae, Mogibacteriaceae, Moraxellaceae, Mycobacteriaceae, Myxococcaceae, Nakamurellaceae, Nannocystaceae, Nitrosomonadaceae, Nitrospiraceae, Nocardiaceae, Nocardioidaceae, Oscillochloridaceae, Oxalobacteraceae, Oxalobacteraceae, Paenibacillaceae, Parachlamydiaceae, Patulibacteraceae, Pelobacteraceae, Peptostreptococcaceae, Phyllobacteriaceae, Piscirickettsiaceae, Planococcaceae, Polyangiaceae, Procabacteriaceae, Promicromonosporaceae, Propionibacteriaceae, Pseudomonadaceae, Pseudonocardiaceae, Rhizobiaceae, Rhodobacteraceae, Rhodobiaceae, Rhodocyclaceae, Rhodospirillaceae, Rickettsiaceae, Rikenellaceae, Roseiflexaceae, Saccharibacteria_genera_incertae_sedis, Sanguibacteraceae, Saprospiraceae, Sinobacteraceae, Solibacteraceae, Solirubrobacteraceae, Sphingobacteriaceae, Sphingomonadaceae, Spirochaetaceae, Sporichthyaceae, Sporolactobacillaceae, Staphylococcaceae, Streptomycetaceae, Streptosporangiaceae, Symbiobacteriaceae, Syntrophobacteraceae, Syntrophomonadaceae, Thermaceae, Thermoactinomycetaceae, Thermoanaerobacteraceae, Thermogemmatisporaceae, Thermomonosporaceae, Tissierellaceae, Turicibacteraceae, Veillonellaceae, Weeksellaceae, Williamsiaceae, Xanthobacteraceae, Xanthomonadaceae, Acaryochloridaceae, Alcaligenaceae, Alcanivoracaceae, Alteromonadaceae, Aquificaceae, Bacillaceae, Bacteroidaceae, Bradyrhizobiaceae, Burkholderiaceae, Campylobacteraceae, Carnobacteriaceae, Caulobacteraceae, Chlorobiaceae, Chloroflexaceae, Chromatiaceae, Chromatiales, Coeloplanidae, Co leofasciculaceae, Cyclobacteriaceae, Deferribacteraceae, Desulfobacteraceae, Desulfurellaceae, Ectothiorhodospiraceae, Erythrobacteraceae, Ferrimonadaceae, Flammeovirgaceae, Flavobacteriaceae, Aphanizomenonaceae, Aurantimonadaceae, Bacillaceae, Chitinophagaceae, Chromatiaceae, Comamonadaceae, Cyanothecaceae, Flaviobacteriaceae, Fusobacteriaceae, Halieaceae, Haloplasmataceae, Hyphomonadaceae, Intrasporangiaceae, Magnetococcaceae, Micrococcaceae, Nautiliaceae, Oceanospirillaceae, Phyllobacteriaceae, Piscirickettsiaceae, Pseudoalteromonadaceae, Pseudococcidae, Psychromonadaceae, Rhodobacteraceae, Sphingomonadaceae, Streptococcaceae, Synechococcaceae, Thermodesulfobacteriaceae, Thermotogaceae, Vibrionaceae, Flexibacteraceae, Haliangiaceae, Halobacteriaceae, Halomonadaceae, Helicobacteraceae, Hydrogenothe, maceae, Hyphomonadaceae, Idiomarinaceae, Intrasporangiaceae, Kordiimonadaceae, Lentisphaeraceae, Mariprofundaceae, Methanobacteriaceae, Methylococcaceae, Microbacteriaceae, Micromonosporaceae, Moraxellaceae, Myxococcaceae, Nautiliaceae, Nitrosopumilaceae, Nocardiaceae, Oceanospirillaceae, Paenibacillaceae, Parvularculaceae, Pelagibacteraceae, Pelobacteraceae, Peptococcaceae, Phyllobacteriaceae, Piscirickettsiaceae, Planctomycetaceae, Propionibacteriaceae, Pseudonocardiaceae, Rhizobiaceae, Rhodospirillaceae, Rhodothermaceae, Rivulariaceae, Saprospiraceae, Shewanellaceae, Sinorhizobium, Sphingomonadaceae, Spirochaetaceae, Synechococcaceae, Thermoanaerobacteraceae, Thermococcaceae, Thermotogaceae, Thermotogaceae, Verrucomicrobiae, Vibrionaceae, Xanthomonadaceae, Peridiniphycidae, Suessiaceae, Pyrocystaceae, Lophodiniaceae, Gloeodiniaceae, Tovelliaceae, Prorocentraceae, Gonyaulacaceae, Gymnodiniaceae, Hemidiniaceae, Symbiodiniaceae, Glenodiniopsidaceae, Blastodiniaceae, Goniodomataceae, Peridiniaceae, Ostreopsidaceae, Pyrophacaceae, Kareniaceae, Ceratiaceae, Ceratocoryaceae, Heterocapsaceae, Gonyaulax, Polykrikaceae, Oxytoxaceae, Ptychodiscaceae, Peridiniales, Gymnodiniales, Araphid-pennate, Bacillariophyta, Bangiaceae, Bathycoccaceae, Batrachospermales, Bo lidophyceae-and-relatives, Bonnemaisoniaceae, Braarudosphaeraceae, Callithamniaceae, Calyptrosphaeraceae, Ceramiaceae, Chaetopeltidales, Chaetophorales, Chlorarachnida, Chlorellales, Chlorodendrales, Chlorophyceae, Chlorophyta, Chrysochromulinaceae, Chrysoculteraceae, Chrysomerophyceae, Chrysophyceae-Synurophyceae, Cladophorales, Coccolithaceae, Coccolithales, Corallinales, Crustomastigaceae, Cryptomonadales, CW-Chlamydomonadales, Cyanidiales, Cyanophoraceae, Cyanoptycaceae, Dictyochales, Dictyochophyceae, Dinophyceae, Dolichomastigaceae, Do lichomastigales, Embryophyceae, Erythropeltidales, Euglenales, Euglenida, Eustigmatophyceae, Eutreptiales, Florenciellales, Florideophyceae, Gigartinales, Gonyaulacales, Mamiellaceae, Mamiellales, Mamiellophyceae, Marsupiomonadales, Mesostigmatophyceae, Microthamniales, Monomastigales, Nephroselmidaceae, Oedogoniales, Olisthodiscus, Oltmansiellopsidales, Pavlovaceae, Pedinellales, Pedinomonadales, Pedinophyceae, Pelagophyceae, Peridiniales, Phaeocystaceae, Phaeophyceae, Phaeothamniales, Pinguiochrysidaceae, Pleurochrysidaceae, Polar-centric-Mediophyceae, Porphyridiales, Prasinococcales, Prasiolales, Prorocentrales, Prymnesiaceae, Prymnesiophyceae, Pyramimonadales, Radial-centric-basal-Coscinodiscophyceae, Raphid-pennate, Raphidophyceae, Rhizochromulinales, Rhodellales, Rhodomelaceae, Rhodophyta, Rhodymeniales, Sphaeropleales, Spyridiaceae, Stylonemataceae, Suessiales, Synurales, Thoracosphaeraceae, Trebouxiophyceae, Trentepohliales, Ulotrichales, Ulvales-relatives, Vitrella, Watanabea-Clade, Wrangeliaceae, Xanthophyceae, Zygnemophyceae.

Non-limitative examples of macroorganism extracts which can be screened for a modulation of RNA silencing activity using the method of the invention are derived from algae, plants, insects or animals.

An additional step (d) allows the characterization of the effects of said molecules, microorganisms or extracts on PTGS enhancement and the quantification of the intensity by which they modulate RNA silencing in tissues that are relevant for pathogen entry, propagation or replication.

This additional step (d) is carried out by monitoring the levels of artificial siRNAs derived from said inverted-repeat and/or endogenous small RNAs and of artificial and/or endogenous small RNA targets.

For example, the levels of the 20-24 nt small RNA duplexes arising by the processing of the inverted repeat RNA RNase-III enzymes DICERs are monitored.

These level analyses will determine (i) at which steps of the RNA silencing pathway a given molecule, microorganism or extract is acting (small RNA biogenesis, accumulation and/or activity) (ii) the intensity by which a given molecule, microorganism or extract is modulating RNA silencing. Regarding the quantification of artificial or endogenous small RNA accumulation, Low Molecular Weight (LMW) Northern blot analyses or Real Time quantitative PCR (RT-qPCR) analyses can be used. Concerning the quantification of artificial or endogenous small RNA targets, High Molecular Weight (HMW) Northern analyses or RT-PCR analyses can be used.

Another subject-matter of the invention is a method for characterizing the mode of action of natural or synthetic molecules, microorganism and extracts from micro- or macro-organisms that are known to enhance plant disease resistance comprising the following steps:

-   -   (a) providing several types of visual PTGS reporter plants         transgenic for an inverted-repeat construct which triggers         post-transcriptional gene silencing of an endogenous visual         reporter gene, each type driven by a different tissue-specific         promoter wherein said tissue is relevant for pathogen entry,         propagation or replication,     -   (b) applying said molecules, microorganisms or extracts on said         plants,     -   (c) visually observing plant changes translating an increase or         decrease of said post-transcriptional gene silencing activity of         said endogenous visual reporter gene in one or several of said         types of visual PTGS reporter plants.

An additional step (d) allows the identification of molecules, microorganisms or extracts that have a tissue-specific effect or an effect on different tissues that are relevant for pathogen entry, propagation or replication.

This additional step (d) is carried out by comparing the visual effect between said types of visual PTGS reporter plants

(i) wherein a tissue-specific effect means that said molecules, microorganisms or extracts are relevant for pathogens which entry, propagate or replicate only by said tissue or

(ii) wherein an effect on different tissues means that said molecules, microorganisms or extracts are relevant for pathogens with different modes of entry, propagation or replication.

In one embodiment, post-transcriptional gene silencing is RNA silencing.

Said visual PTGS reporter plants are wild-type plants which have been transformed by a vector comprising an inverted-repeat construct. Said inverted-repeat construct, preferably a DNA sequence giving rise to a dsRNA polynucleotide with a hairpin structure, comprises an inverted-repeat of corresponding cDNA of said endogenous visual reporter gene or a fragment thereof. This inverted-repeat carries an intron sequence in the middle between the repeats to facilitate the folding of the dsRNA.

The inverted-repeat construct is under the control of a relevant tissue-specific promoter that is active enough to visualize phenotypic change due to the silencing of the endogenous visual reporter gene “Relevant” and “active enough” means that (i) the activity of the promoter has to be highly specific to the given tissue but also strong enough to produce small RNAs that trigger a visually detectable chlorosis within and around the given tissue; (ii) the promoter has to be as less as possible responsive to hormone or pathogen elicitors.

The inverted-repeat construct triggers post-transcriptional gene silencing of an endogenous visual reporter gene.

Preferably, the inverted-repeat construct comprises a sense and an antisense sequences, possibly separated by an intron or a fragment of an intron.

Most preferably, the inverted-repeat construct comprises the sense and antisense sequences of the SUL gene.

The sense sequence has a high degree of homology with the cDNA of the endogenous visual reporter gene, preferably more than 90%, more preferably more than 95%, the most preferably more than 99% of homology.

Preferably, the sense sequence is the cDNA of the endogenous visual reporter gene or a fragment thereof.

Said tissue-specific promoter is preferably selected in the group consisting of AAP6-p, IRX3-p, GC1-p, HYD-p, MYB60-p, CAB3-p, MYC1-p, WOX4-p and AHA3-p.

The inverted-repeat RNA polynucleotide is processed in said transgenic plants into siRNA duplexes.

These artificial siRNAs modulate the expression of said wild-type endogenous visual reporter gene expressed by said plants.

If PTGS is enhanced, post-transcriptional gene silencing of said endogenous visual reporter gene is increased and the expression of said endogenous visual reporter gene is thus decreased.

If PTGS is decreased, post-transcriptional gene silencing of said endogenous visual reporter gene is decreased and the expression of said endogenous visual reporter gene is thus increased.

For example with an endogenous visual reporter gene involved in chlorophyll biosynthesis in leaves:

-   -   if PTGS is enhanced, the expression of said endogenous visual         reporter gene is decreased and an enhanced visual chlorotic         phenotype appears wherein and/or nearby tissues/cell types where         the inverted-repeat is expressed i.e. in the target tissue of         said tissue-specific promoter,     -   if PTGS is decreased, the expression of said endogenous visual         reporter gene is increased and a weaker chlorotic phenotype is         observed wherein and/or nearby tissues/cell types where the         inverted-repeat is expressed i.e. in the target tissue of said         tissue-specific promoter.

For example with an endogenous visual reporter gene involved in chlorophyll biosynthesis in leaves and a promoter specific of hydathode tissues:

-   -   if PTGS is enhanced, the expression of said endogenous visual         reporter gene is decreased and an enhanced chlorotic phenotype         appears at the level of and/or nearby hydathodes,     -   if PTGS is decreased, the expression of said endogenous visual         reporter gene is increased and a weaker chlorotic phenotype is         observed at the level of and/or nearby hydathodes.

In step (b), said molecule, microorganism or extract can be applied either at seedling stage or at later developmental stages such as at rosette stage. This molecule, microorganism or extract is applied either in liquid medium in (micro) well-plates, by infiltration using a needle-less syringe or vacuum, or by spray using a concentration of surfactant that is known from people skilled in the art.

Visual observation of step (c) can be made several days, preferably 4 to 5 days, after step (b) The term “silencing” means down-regulating or antagonizing, at least partly, a targeted gene transcript.

In one embodiment, said silencing of the method according to the invention is temporary.

“Temporary” means reversible in several weeks, preferably several days.

Another subject-matter of the present invention is a transgenic plant comprising an inverted-repeat construct which triggers post-transcriptional gene silencing of an endogenous visual reporter gene driven by a tissue-specific promoter wherein said tissue is relevant for pathogen entry, propagation or replication and active enough in the dedicated tissues or cell types targeted

Preferably, said tissue relevant for pathogen entry, propagation or replication is relevant for pathogen entry and/or short distance propagation and/or long distance propagation and/or replication.

Preferably, said tissue relevant for pathogen entry is selected in the group consisting of hydathodes, guard cells, the base of trichomes and epidermal cells.

Preferably, said tissue relevant for short or long distance propagation of pathogens in the vasculature is selected in the group consisting of cambium cells, xylem parenchyma cells or phloem companion cells.

Preferably, said tissue relevant for pathogen replication is selected in the group consisting of mesophyll cells.

Preferably, said endogenous visual reporter gene is involved in pigment biosynthesis, preferably in chlorophyll biosynthesis, preferably in aerial part of said plants.

More preferably, said endogenous visual reporter gene is the Chlorina42 (CH42) gene, known also as the SULPHUR (SUL) gene. Its cDNA is SEQ ID NO:1.

Preferably, said plants are selected in the group consisting of model plants, preferably Arabidopsis thaliana or agronomical plants, preferably cereals.

Preferably, said pathogen is selected in the group consisting of bacteria, fungi, oomycetes and viruses.

Preferably, said inverted-repeat construct is SEQ ID NO:2.

In one embodiment, said tissue-specific promoter is selected in the group consisting of AAP6 promoter of SEQ ID NO:4, IRX3 promoter of SEQ ID NO:5, GC1 promoter of SEQ ID NO:6, HYD promoter of SEQ ID NO:7, AHA3 promoter of SEQ ID NO: 8, MYC1 promoter of SEQ ID NO: 9, MYB60-derived promoter of SEQ ID NO: 10, CAB3 promoter of SEQ ID NO: 11, WOX4 promoter of SEQ ID NO: 12, BDG promoter of SEQ ID NO:37.

Another subject-matter of the present invention is an isolated dsRNA with a hairpin structure comprising an inverted-repeat construct which triggers post-transcriptional gene silencing of an endogenous visual reporter gene under the control of a tissue-specific promoter.

Another subject-matter of the present invention is an isolated dsRNA with a hairpin structure comprising SEQ ID NO:2 under the control of a tissue-specific promoter.

Another subject-matter of the present invention is an isolated dsRNA with a hairpin structure of SEQ ID NO:3.

Another subject-matter of the present invention is a vector comprising an isolated dsRNA with a hairpin structure comprising SEQ ID NO:2 under the control of a tissue-specific promoter or an isolated dsRNA with a hairpin structure of SEQ ID NO:3.

Examples Material and Methods DNA Constructs

To generate the plasmids expressing a hairpin of the SUL gene (AT4G18480) under the control of a tissue-specific promoter, a MultiSite Gateway® (Invitrogen) strategy was used. The tissue-specific promoters (AAP6-p, IRX3-p, GC1-p, HYD-p, WOX4-p, CAB3-p, MYC1-p, MYB60-p, BDG-p and AHA3-p) were amplified by 2 steps-PCR with specific primers (see Table n° 1) using genomic DNA isolated from Arabidopsis thaliana leaves. The resulting PCR were introduced into the pDON vector pDON221_P1P5r (Invitrogen) using the BP clonase enzyme mix (Invitrogen).

To generate the plasmid encoding for the SUL hairpin (pDON221_SUL-LUS), PCR product of 200 nt containing NcoI site was generated with specific primers (see Table n° 1) using pK7WG2D as a template. The resulting PCR product was introduced into the pDON221_P5P2 (Invitrogen) to give pDON221_P5P2_NcoI. The SUL hairpin fragment was purified from the NcoI-digested plasmid atSUC2-SUL-LUS (Himber et al., 2003). The resulting fragment was inserted as a NcoI restriction fragment into pDON221_P5P2_NcoI. Each plasmid containing a tissue-specific promoter is recombined in presence of pDON221_SUL-LUS and the pDEST plasmid pB7WG (Karimi et al., 2002) using the LR clonase plus enzyme mix (Invitrogen) to give the following plasmids: AAP6-p::SUL-LUS, IRX3-p::SUL-LUS, HYD-p::SUL-LUS, GC1-p::SUL-LUS, WOX4-p::SUL-LUS, CAB3-p::SUL-LUS, MYC1-p::SUL-LUS, MYB60-p::SUL-LUS and AHA3-p::SUL-LUS.

Transgenic Plants

Arabidopsis thaliana grp7-1, rdr6, dcl2dcl4 and hen1-1 were described previously (Zu et al., 2007; Xie et al., 2005; Chen et al., 2002)

Transformation of the AAP6-p::SUL-LUS, IRX3-p::SUL-LUS, HYD-p::SUL-LUS, GC1-p::SUL-LUS, WOX4-p::SUL-LUS, MYC1-p::SUL-LUS, MYB60-p::SUL-LUS, BDG-p::SUL-LUS and AHA3-p::SUL-LUS constructs in Col-0 with Agrobacterium strain GV3101 was performed as described previously (Bechtold et al., 1993). Selection was on medium containing 10 mg/l DL-Phosphinothricin (Sigma aldrich). Pictures of 4-weeks old T1 transgenic plants were taken.

Bacterial Infection

Pseudomonas syringae pv. tomato DC3000 (Pto DC3000) carrying a GFP-encoding plasmid (Badel et al., 2002) was grown at 28° C. in NYGB medium (5 g L⁻¹ bactopeptone, 3 g L⁻¹ yeast extract, 20 ml L⁻¹ glycerol) containing rifampicin (25 mg mL⁻¹) for selection.

Bacteria infections were performed by spray inoculation or by wound inoculation in secondary veins. For the spray assay, the bacteria Pto DC3000-GFP was used at 2·10⁷ cfu/ml supplemented with 0.005% of Silwet L-77 (Lehle Seeds). For wound inoculation, Pto DC3000-GFP was used at 5·10⁷ cfu/ml and inoculated in secondary veins using a toothpick. The plants were covered with a lid during all the time of the experiment. GFP is monitored under UV light at 2 days (FIG. 1A) or 5 days (FIG. 1B) post inoculation (dpi).

Pseudomonas fluorescens was inoculated by infiltration at 1·10⁸ cfu/ml into the leaves. Forty-eight hours later, the infiltrated leaves were collected and chlorophyll was cleared by using lactophenol (lactic acid:glycerol:water:phenol; 1:1:1:1). Leaves were then incubated with 3,3′-Diaminobenzidine (1 mg·ml⁻¹; pH 3.5) for 3 hours to stain hydrogen peroxide (H₂O₂) molecules.

TABLE NO 1 Oligonucleotides used for clonings. SEQ Name of the plasmid Name of oligos Sequence of the oligos ID NO: pDON_P1P5r_pAAP6 pDON_P1_pAAP6_F AAAAAGCAGGCT gctgatgctgttattaatagt 13 pDON_P5r_pAAP6_R TATACAAAGTTG ctatcgattgtattgagctta 14 pDON_P1P5r_pHYD pDON_P1_pHYD_F AAAAAGCAGGCT aagttaggacaacacgcaaa 15 pDON_P5r_pHYD_R TATACAAAGTTG tggagattctcacccgcat 16 pDON_P1P5r_pIRX3 pDON_P1_pIRX3_F AAAAAGCAGGCT cagaattcaagtagctgccca 17 pDON_P5r_pIRX3_R TATACAAAGTTG agggacggccggagatta 18 pDON_P1P5r_pGC1 pDON_P1_pGC1_F AAAAAGCAGGCT tttggaacactctaccaacg 19 pDON_P5r_pGC1_R TATACAAAGTTG atacttgagtagtgatatgaa 20 pDON_P1P5r_pWOX4 pDON_P1_WOX4_F AAAAAGCAGGCT ggcaagtgtagtggaggagg 21 pDON_P5r_WOX4_R TATACAAAGTTG tgctatatgttaaaactagcaaatgc 22 pDON_P1P5r_pAHA3 pDON_P1_pAHA3_F AAAAAGCAGGCT aataactacgtatatgctgggaag 23 pDON_P5r_pAHA3_R TATACAAAGTTG gtggactacgttaggctatttg 24 pDON221_P5P2_NcoI pDON_P5_Kan_NcoI_F ATACAAAAGTTG aggatgatctggacgaagag 25 pDON_P2_Kan_NcoI_R AGAAAGCTGGGT tgtcctgatagcggtccgc 26 adap_attB2 GGGGACCACTTTGTACAAGAAAGCTGGGT 27 adap_attB5 GGGGACAACTTTGTATACAAAAGTTG 28 adap_attB1 GGGGACAAGTTTGTACAAAAAAGCAGGCT 29 adap_attB5r GGGGACAACTTTTGTATACAAAGTTG 30 pDON_P1P5r_pMYC1 pDON_P1_pMYC1_F AAAAAGCAGGCT gaggttcaaatcaatatgaaatcc 31 pDON_P5r_pMYC1_R TATACAAAGTTG aggagacaaccaaaaggcaaaat 32 pDON_P1P5r_pMYB60 pDON_P1_pMYB60_F AAAAAGCAGGCT cgtgtggagatcaacatatcttc 33 pDON_P5r_pMYB60_R TATACAAAGTTG catctctctctctcttcctc 34 pDON_P1P5r_pCAB3 pDON_P1_pCAB3_F AAAAAGCAGGCT aaatcaagagaaaatgtgattctcg 35 pDON_P5r_pCAB3_R TATACAAAGTTG gattgaaaatggttaggtagggtt 36 pDON_Pl_pBDG pDON_P1_pBDG_F AAAAAGCAGGCTgatgccacgcacacgtcc 38 pDON_P5r_pBDG_R TATACAAAGTTGgctgtggagatgagtcagt 39

EXAMPLES Example 1: PTGS Restricts Pathogen Entry and Propagation

Hydathodes and stomata are two major entry sites for endophytic colonization of foliar pathogens. Stomata are small pores located on the leaf surface that are surrounded by pairs of specialized parenchyma cells termed guard cells that regulate the aperture and closure of stomata to facilitate exchange of gases with the environment. Hydathodes are stomata-like structures located at the margin or tips of plant leaves. They are supposedly permanently open water pores that are closely associated with the ends of the leaf vascular system. Importantly, plants have evolved sophisticated active defense mechanisms to prevent pathogen entry at the level of hydathodes and stomata, and pathogen propagation in the vasculature. For instance, the recognition of the non-pathogenic bacteria Pseudomonas fluorescens leads to a strong production of hydroxide peroxide (H₂O₂) molecules at the level of hydathodes, guard cells and within and around the vasculature likely to limit the entry and propagation of bacterial pathogens and perhaps other type of pathogens (FIGS. 1A, B and C). However, the role of PTGS in orchestrating such defense responses remains elusive. To determine the physiological relevance of PTGS in restricting pathogen entry, the inventors have first analyzed the ability of the model pathogenic bacterium Pseudomonas syringae pv. tomato strain DC3000 (Pto DC3000) to enter through hydathodes and stomata from Arabidopsis WT and PTGS-defective mutant leaves. For this purpose, they have spray inoculated 5-week-old leaves from Arabidopsis WT, hen1-1 and grp7-1 mutants—both hen1-1 and grp7-1 mutant are impaired in RNA silencing—with a virulent Pto DC3000 strain expressing the Green Fluorescence Reporter (GFP) protein and have further monitored the GFP signal during the course of the infection under UV light. Interestingly, results from these analyses revealed a pronounced GFP signal in hydathodes of hen1-1-infected mutant leaves as early as 2 day-post inoculation (dpi) that was absent from hydathodes of WT-infected leaves (FIG. 2A). Enhanced GFP signal was also obtained within and around stomata from grp7-1-infected leaves as compared to WT-infected leaves at 2 dpi (FIG. 2A). Overall, these results indicate that PTGS plays a major role in restricting the entry of Pto DC3000 at both the level of hydathodes and stomata. These results also suggest that PTGS is likely active in these tissues/cell types as previously reported in guard cells (Yang et al., 2008).

Once inside the intercellular space of plant leaves, foliar biotrophic pathogens use different strategies to colonize distal plant tissues. For example, RNA viruses use alive phloem tissues as a major route to propagate in systemic tissues and this viral spreading is restricted by PTGS. As an example, Arabidopsis mutants that are defective in the two major antiviral Dicer-like 2 (DCL2) and DCL4 exhibit long distance propagation of several RNA viruses (Deleris et al., 2006; Diaz-Pendon et al., 2007; Qu et al., 2008). By contrast, fungal, oomycete and bacterial pathogens can spread in distal plant tissues through xylem vessels, which are dead cells that transport nutrients and water from the root to the aerial part of the plant. However, it is not known whether PTGS plays any role in restricting the propagation of such non-viral pathogens within and around xylem vessels. To test this idea, the inventors have wound-inoculated leaf secondary veins from WT and the PTGS-defective mutants dcl2/dcl4 and rdr6-15 with the virulent Pto DC3000-GFP strain, which propagates exclusively through Arabidopsis xylem vessels (Yu et al., 2013), and have further monitored GFP signal along the leaf vascular tissues of these different genotypes. Results from these analyses revealed a significant increase in bacterial spreading in both dcl2/dcl4 and rdr6-15-infected mutant leaves as compared to WT-infected leaves (FIG. 2B), which was associated with enhanced disease symptoms in tissues that surround the leaf vasculature of these PTGS-defective mutants (FIG. 2C). These results indicate that PTGS plays also a critical role in restricting Pto DC3000 propagation within and around leaf vasculature. Furthermore, they suggest that PTGS might be active in tissues/cell types that surround xylem vessels such as xylem parenchyma cells, cambial cells and phloem tissues, which is consistent with previous reports showing that IR-PTGS is effective in phloem companion cells (Smith et al., 2010; Dunoyer et al., 2005; de Felippes et al., 2011).

Example 2: Silencing of the SUL Endogene is Effective in Tissues/Cell Types that are Relevant for Pathogen Entry and Propagation Providing that a Promoter that is Specific and Active Enough is Used to Drive the Expression of the Inverted Repeat

The results obtained in Example 1 prompted the inventors to generate PTGS sensors in tissue/cell types that are physiologically relevant for pathogen entry and/or propagation. Additionally, they decided to generate PTGS sensors in cell types that are relevant for pathogen replication i.e mesophyll cells and for the entry of the majority of fungal or oomycete pathogens i.e epidermal cells. Given that plants produce a variety of small RNA-dependent PTGS pathways that involve common or specific plant silencing factors, they decided to generate biosensors from a well-characterized PTGS pathway that is functionally relevant for biotic stress responses: the inverted repeat PTGS (IR-PTGS) pathway. These PTGS sensors were all designed to silence the SUL (At4g18480) endogene in hydathodes, guard cells, xylem parenchyma cells, vascular meristematic cells (cambial cells), phloem companion cells, cells surrounding the base of trichomes or mesophyll cells. All these tissue- or cell type-specific PTGS sensors were produced in the reference Arabidopsis accession Columbia (Col-0).

To generate IR-PTGS sensors, the inventors have first generated constructs containing an hairpin that carries sequence homology with the SUL endogene under the control of the tissue- or cell type-specific xylem promoter, guard cell promoter, hydathode promoter, cambium promoter, mesophyll promoter and base of trichome promoter. Among the Arabidopsis encoding genes, the inventors selected tissue-specific promoters that fulfil several criteria: (i) the activity of the promoter has to be highly specific to the given tissue but also strong enough to produce small RNAs that trigger a visually detectable chlorosis in the given tissue; (ii) the promoter has to be as less as possible responsive to hormone or pathogen elicitors. After extensive bibliographic research and analyses of mRNA-seq datasets, the inventors selected the following promoters: AAP6 promoter: active in xylem parenchyma cells and in meristematic vascular cells (Okumoto et al., 2002), IRX3 promoter: active in xylem parenchyma cells (Gardiner et al., 2003), GO and MYB60 promoters: active in guard cells (Yang et al., 2008), AtmiR164A truncated promoter: active in hydathodes (Nikovics et al., 2006), WOX4 promoter: active in meristematic vascular cells (Hirakawa et al., 2010), MYC1 promoter: active at the base of trichome (Zhao et al., 2012), AHA3 promoter: active in phloem companion cells (DeWitt et al., 1991), BDG promoter: active in epidermal cells (Kurdyukov et al., 2006) or CAB3 promoter: active in mesophyll cells (Susek et al., 1993). It is noteworthy that the SUL hairpin has been previously described and triggers IR-PTGS through well-characterized Arabidopsis silencing factors such as DCL4 and AGO1 (Dunoyer et al., 2005; Brodersen et al., 2008). All these constructs were further cloned into the binary vector pB7WG and transformed in the Arabidopsis Col-0 accession. Examples of the phenotypes obtained from the WOX4-p:IR-SUL, the AAP6-p:IR-SUL, the IRX3-p:IR-SUL and the GC1-p:IR-SUL and the miR164A-p:IR-SUL primary transformants are depicted in FIG. 3B. Interestingly, all these Arabidopsis reference lines, except WOX4-p:IR-SUL, display a chlorotic phenotype in the tissues and cell types of interest (FIG. 3B), as well as in cells that surround the siRNA production site (data not shown), which is consistent with previous reports showing non-cell autonomous effects triggered by artificial siRNAs directed against the SUL gene (Dunoyer et al., 2005; de Felippes et al., 2011). Overall, these results indicate that IR-PTGS is effective in hydathodes, xylem tissues and guard cells. The authors were not able to detect visually a chlorotic phenotype in homozygous WOX4-p:IR-SUL transgenic plants (FIG. 3B). Several reasons can account for the absence of chlorosis: (i) the WOX4 promoter activity is not strong enough to produce the minimal amount of small RNA required to trigger IR-PTGS mediated chlorosis or (ii) IR-PTGS is not effective in the vascular cambium. For this reason, the authors selected other promoters such as the AAP6 promoter that is significantly expressed in both cambial cells and xylem parenchyma cells. These biosensors are thus valuable resources to monitor IR-PTGS activity in tissues and/or cell types that are relevant for pathogen entry, propagation or replication.

Example 3: Proof-of-Concept Experiment: Formulated and Active Compounds that are Known to Promote Disease Resistance in Agriculturally Important Crops can Elevate PTGS Activity on a Specific Arabidopsis Silencing Reporter

To determine whether the above Arabidopsis PTGS sensors represent promising biosensors to identify solutions to enhance disease resistance, the inventors have tested whether formulated or active compounds, which are known to induce plant disease resistance in cultivated plants, can also enhance PTGS activity on the above silencing reporter systems. For this purpose, they have sprayed a previously characterized phloem-specific IR-PTGS sensor (Dunoyer et al., 2005) with either (1) Salicylic acid (SA), a well-characterized phytohormone that plays a critical role in resistance against biotrophic pathogens, (2) 2,6-dichloroisonicotonic acid and benzo-(1,2,3)-thiadiazole-7-carbothioic acid S-methyl ester (BTH), a functional analog of SA that is regularly used by farmers to enhance disease resistance in crops, (3) Aliette, formulated fosetyl-Aluminium that can stimulate plant antimicrobial defense in cultivated plants but also protect them from fungal and oomycete infections through a potent and systemic fungicide activity, (4) Serenade, which is composed of formulated Bacillus subtilis (5) formulated Laminarine, a beta 1-3 glucan that mimics fungal cell wall and therefore promote natural antifungal defense responses in some cultivated plants; and have further monitored the effects of such treatments on the vein-centered chlorotic phenotype of this IR-PTGS reporter system. Interestingly, with the exception of Serenade (FIG. 4), all the above treatments led to a significant enhanced chlorotic phenotypes indicating stronger IR-PTGS activity in these challenged plants (FIGS. 4, 5 and 6). It is noteworthy that Aliette was the most potent inducer of IR-PTGS as revealed by a very strong and spreading chlorotic phenotype throughout the IR-PTGS sensor leaves, even at low concentrations, while the formulated Laminarine compound gave a mild but yet detectable enhanced chlorotic phenotype (FIG. 4 and data not shown). Further molecular analyses conducted in the SA-treated leaf samples revealed a significant decrease in SUL protein levels with a mild reduction in SUL transcript accumulation (FIG. 5), supporting a role for SA in promoting IR-PTGS activity particularly by inhibiting protein production. Moreover, no significant effect on the accumulation of artificial siRNAs was observed upon SA treatment at the concentration used (data not shown). It is noteworthy that the presented molecular analyses allow us (i) to detect at which steps of the PTGS a given molecule is acting (small RNA biogenesis and/or RISC activity) (ii) to quantify the strength by which the candidate molecules is modulating RNA silencing in a given tissue that is relevant for disease management. We thus conclude that these reporters can be used not only to easily and rapidly identify compounds that modulate RNA silencing—through a modulation of the chlorotic phenotype—but also to quantify their effects on RNA silencing activity and likewise on plant immunity (compounds that will have the potential to significantly enhance plant immune responses will likely be the ones that trigger a strong chlorotic phenotype and a strong decreased accumulation in the SUL and endogenous small RNA target levels).

To test whether the increase level of PTGS detected in SA-treated phloem-specific IR-PTGS sensor is detectable to other tissues, the inventors have sprayed different tissue-specific biosensors with the same concentration of SA. The biosensors specific to hydathodes, xylem parenchyma cells, guard cells and companion cells of phloem were sprayed with SA and the level of chlorosis was assessed 5 day later (FIG. 6). Interestingly, the above treatment led to a significant enhanced chlorotic phenotype only on the phloem-specific reporter but not in other silencing reporter tested (FIG. 6) suggesting that SA treatment induces PTGS activity specifically into phloem tissue. Therefore, all the leaf tissues do not respond similarly to a given molecule indicating that a molecule can induce PTGS in a tissue-specific manner. These observations therefore highlight the importance of using different tissue-specific biosensors to screen natural or synthetic compounds, microorganisms, macro- or micro-organism extracts that can have a PTGS inducer activity specifically in a given tissue that is relevant to manage a specific disease. On the contrary, we are anticipating that the whole series of reporters will be also exploited to identify molecules, microorganisms or extracts that can induce PTGS/immune responses in all the above tissues. Such compounds, microorganisms or extracts will have the potential to confer broad-spectrum disease resistance and to restrict growth of pathogens with different modes of entry, propagation and replication. They will thus be the most relevant to increase disease resistance against a wide range of pathogens with different lifestyles.

Overall, these results provide ‘proof-of-concept’ data for the use of the above tissue/cell type specific IR-PTGS sensors to determine the mode of action of natural or synthetic compounds that are known to promote disease resistance in cultivated plants. Furthermore, given that (i) the tissue/cell type specific chlorotic phenotypes are detectable at seedlings stage (data not shown) (ii) the gain of PTGS activity is easily scorable in response to active or formulated compounds within few days post-treatment (FIGS. 4, 5 and 6), the above IR-PTGS sensors are thus well-suited for high-throughput screening of natural or synthetic compounds that can promote disease resistance in cultivated plants by enhancing PTGS activity.

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1. Method for screening natural or synthetic molecules, microorganisms or extracts from micro- or macro-organisms for their potential ability to inhibit pathogen entry, propagation or replication in plants through PTGS enhancement comprising the following steps: (a) providing visual PTGS reporter plants transgenic for an inverted-repeat construct which triggers post-transcriptional gene silencing of an endogenous visual reporter gene driven by a tissue-specific promoter wherein said tissue is relevant for pathogen entry, propagation or replication, (b) applying said molecules, microorganism or extracts on said plants, (c) visually observing plant changes translating an increase or decrease of said post-transcriptional gene silencing activity of said endogenous visual reporter gene.
 2. Method according to claim 1 for characterizing the effects of said molecules, microorganisms or extracts on PTGS enhancement and for quantifying the intensity by which they modulate RNA silencing in tissues that are relevant for pathogen entry, propagation or replication comprising an additional step (d) (d) monitoring the levels of artificial siRNAs derived from said inverted-repeat and/or endogenous small RNAs and of artificial and/or endogenous small RNA targets.
 3. Method for characterizing the mode of action of natural or synthetic molecules that are known to enhance plant disease resistance comprising the following steps: (a) providing several types of visual PTGS reporter plants transgenic for an inverted-repeat construct which triggers post-transcriptional gene silencing of an endogenous visual reporter gene, each type driven by a different tissue-specific promoter wherein said tissue is relevant for pathogen entry and/or propagation, (b) applying said molecule on said plants, (c) visually observing plant changes translating an increase or decrease of said post-transcriptional gene silencing activity of said endogenous visual reporter gene in one or several of said types of visual PTGS reporter plants.
 4. Method according to claim 3 for identifying molecules, microorganisms or extracts that have a tissue-specific effect or an effect on different tissues that are relevant for pathogen entry, propagation or replication comprising an additional step (d) (d) comparing the visual effect between said types of visual PTGS reporter plants (i) wherein a tissue-specific effect means that said molecules, microorganisms or extracts are relevant for pathogens which entry, propagate or replicate only by said tissue or (ii) wherein an effect on different tissues means that said molecules, microorganisms or extracts are relevant for pathogens with different modes of entry, propagation or replication by different tissues.
 5. A transgenic plant comprising an inverted-repeat construct which triggers post-transcriptional gene silencing of an endogenous visual reporter gene driven by a tissue-specific promoter wherein said tissue is relevant for pathogen entry, propagation or replication
 6. The method or plant according to any of claims 1 to 5, wherein said endogenous visual reporter gene is involved in pigment biosynthesis, preferably in chlorophyll biosynthesis.
 7. The method or plant of claim 6, wherein said endogenous visual reporter gene is SUL cDNA of SEQ ID NO:1.
 8. The method or plant according to any of claims 1 to 7, wherein said relevant tissue for pathogen entry and/or propagation is selected in the group consisting of hydathodes, guard cells, xylem parenchyma and cambium cells, xylem parenchyma cells, cells at the base of trichomes, mesophyll cells and epidermal cells.
 9. The method or plant according to any of claims 1 to 8, wherein said plants are selected in the group consisting of model plants, preferably Arabidopsis thaliana or agronomical plants, preferably cereals.
 10. The method or plant according to any of claims 1 to 9, wherein said pathogen is selected in the group consisting of bacteria, fungi, oomycetes and viruses,
 11. The method or plant according to any of claims 1 to 10, wherein said inverted-repeat construct is SEQ ID NO:2.
 12. The method or plant according to any of claims 1 to 11, wherein said tissue-specific promoter is selected in the group consisting of AAP6 promoter of SEQ ID NO:4, IRX3 promoter of SEQ ID NO:5, GC1 promoter of SEQ ID NO:6, HYD promoter of SEQ ID NO:7, AHA3 promoter of SEQ ID NO: 8, MYC1 promoter of SEQ ID NO: 9, MYB60-promoter of SEQ ID NO: 10, CAB3 promoter of SEQ ID NO: 11, WOX4 promoter of SEQ ID NO:12, BDG promoter of SEQ ID NO:37.
 13. Isolated DNA with a hairpin structure comprising an inverted-repeat construct which triggers post-transcriptional gene silencing of an endogenous visual reporter gene under the control of a tissue-specific promoter.
 14. Isolated DNA with a hairpin structure comprising SEQ ID NO:2 under the control of a tissue-specific promoter.
 15. Isolated DNA with a hairpin structure of SEQ ID NO:3.
 16. Vector comprising an isolated DNA of claim 14 or
 15. 